[876] | 1 | from asap._asap import Scantable |
---|
[226] | 2 | from asap import rcParams |
---|
[1118] | 3 | from asap import print_log |
---|
| 4 | from asap import asaplog |
---|
[946] | 5 | from asap import selector |
---|
[1134] | 6 | from asap import NUM |
---|
[1153] | 7 | from asap import linecatalog |
---|
[102] | 8 | |
---|
[876] | 9 | class scantable(Scantable): |
---|
[102] | 10 | """ |
---|
| 11 | The ASAP container for scans |
---|
| 12 | """ |
---|
[710] | 13 | |
---|
[484] | 14 | def __init__(self, filename, average=None, unit=None): |
---|
[102] | 15 | """ |
---|
| 16 | Create a scantable from a saved one or make a reference |
---|
| 17 | Parameters: |
---|
[181] | 18 | filename: the name of an asap table on disk |
---|
| 19 | or |
---|
| 20 | the name of a rpfits/sdfits/ms file |
---|
| 21 | (integrations within scans are auto averaged |
---|
| 22 | and the whole file is read) |
---|
| 23 | or |
---|
| 24 | [advanced] a reference to an existing |
---|
[102] | 25 | scantable |
---|
[484] | 26 | average: average all integrations withinb a scan on read. |
---|
| 27 | The default (True) is taken from .asaprc. |
---|
| 28 | unit: brightness unit; must be consistent with K or Jy. |
---|
[340] | 29 | Over-rides the default selected by the reader |
---|
| 30 | (input rpfits/sdfits/ms) or replaces the value |
---|
| 31 | in existing scantables |
---|
[710] | 32 | """ |
---|
[976] | 33 | if average is None: |
---|
[710] | 34 | average = rcParams['scantable.autoaverage'] |
---|
[1118] | 35 | #varlist = vars() |
---|
[876] | 36 | from asap._asap import stmath |
---|
| 37 | self._math = stmath() |
---|
| 38 | if isinstance(filename, Scantable): |
---|
| 39 | Scantable.__init__(self, filename) |
---|
[181] | 40 | else: |
---|
[1118] | 41 | if isinstance(filename, str): |
---|
[976] | 42 | import os.path |
---|
| 43 | filename = os.path.expandvars(filename) |
---|
| 44 | filename = os.path.expanduser(filename) |
---|
| 45 | if not os.path.exists(filename): |
---|
| 46 | s = "File '%s' not found." % (filename) |
---|
[718] | 47 | if rcParams['verbose']: |
---|
[976] | 48 | asaplog.push(s) |
---|
| 49 | print asaplog.pop().strip() |
---|
[718] | 50 | return |
---|
[976] | 51 | raise IOError(s) |
---|
[1115] | 52 | if os.path.isdir(filename) \ |
---|
[1118] | 53 | and not os.path.exists(filename+'/table.f1'): |
---|
[976] | 54 | # crude check if asap table |
---|
| 55 | if os.path.exists(filename+'/table.info'): |
---|
[1118] | 56 | ondisk = rcParams['scantable.storage'] == 'disk' |
---|
| 57 | Scantable.__init__(self, filename, ondisk) |
---|
[976] | 58 | if unit is not None: |
---|
| 59 | self.set_fluxunit(unit) |
---|
| 60 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
[718] | 61 | else: |
---|
[1118] | 62 | msg = "The given file '%s'is not a valid " \ |
---|
| 63 | "asap table." % (filename) |
---|
[976] | 64 | if rcParams['verbose']: |
---|
| 65 | print msg |
---|
| 66 | return |
---|
| 67 | else: |
---|
| 68 | raise IOError(msg) |
---|
[226] | 69 | else: |
---|
[1118] | 70 | self._fill([filename], unit, average) |
---|
| 71 | elif (isinstance(filename, list) or isinstance(filename, tuple)) \ |
---|
[976] | 72 | and isinstance(filename[-1], str): |
---|
| 73 | self._fill(filename, unit, average) |
---|
[714] | 74 | print_log() |
---|
[102] | 75 | |
---|
[876] | 76 | def save(self, name=None, format=None, overwrite=False): |
---|
[116] | 77 | """ |
---|
[710] | 78 | Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, |
---|
[280] | 79 | Image FITS or MS2 format. |
---|
[116] | 80 | Parameters: |
---|
[1093] | 81 | name: the name of the outputfile. For format "ASCII" |
---|
| 82 | this is the root file name (data in 'name'.txt |
---|
[497] | 83 | and header in 'name'_header.txt) |
---|
[116] | 84 | format: an optional file format. Default is ASAP. |
---|
[280] | 85 | Allowed are - 'ASAP' (save as ASAP [aips++] Table), |
---|
[194] | 86 | 'SDFITS' (save as SDFITS file) |
---|
[200] | 87 | 'ASCII' (saves as ascii text file) |
---|
[226] | 88 | 'MS2' (saves as an aips++ |
---|
| 89 | MeasurementSet V2) |
---|
[411] | 90 | overwrite: If the file should be overwritten if it exists. |
---|
[256] | 91 | The default False is to return with warning |
---|
[411] | 92 | without writing the output. USE WITH CARE. |
---|
[116] | 93 | Example: |
---|
| 94 | scan.save('myscan.asap') |
---|
[1118] | 95 | scan.save('myscan.sdfits', 'SDFITS') |
---|
[116] | 96 | """ |
---|
[411] | 97 | from os import path |
---|
[226] | 98 | if format is None: format = rcParams['scantable.save'] |
---|
[256] | 99 | suffix = '.'+format.lower() |
---|
[1118] | 100 | if name is None or name == "": |
---|
[256] | 101 | name = 'scantable'+suffix |
---|
[718] | 102 | msg = "No filename given. Using default name %s..." % name |
---|
| 103 | asaplog.push(msg) |
---|
[411] | 104 | name = path.expandvars(name) |
---|
[256] | 105 | if path.isfile(name) or path.isdir(name): |
---|
| 106 | if not overwrite: |
---|
[718] | 107 | msg = "File %s exists." % name |
---|
| 108 | if rcParams['verbose']: |
---|
| 109 | print msg |
---|
| 110 | return |
---|
| 111 | else: |
---|
| 112 | raise IOError(msg) |
---|
[451] | 113 | format2 = format.upper() |
---|
| 114 | if format2 == 'ASAP': |
---|
[116] | 115 | self._save(name) |
---|
| 116 | else: |
---|
[989] | 117 | from asap._asap import stwriter as stw |
---|
[1118] | 118 | writer = stw(format2) |
---|
| 119 | writer.write(self, name) |
---|
[718] | 120 | print_log() |
---|
[116] | 121 | return |
---|
| 122 | |
---|
[102] | 123 | def copy(self): |
---|
| 124 | """ |
---|
| 125 | Return a copy of this scantable. |
---|
| 126 | Parameters: |
---|
[113] | 127 | none |
---|
[102] | 128 | Example: |
---|
| 129 | copiedscan = scan.copy() |
---|
| 130 | """ |
---|
[876] | 131 | sd = scantable(Scantable._copy(self)) |
---|
[113] | 132 | return sd |
---|
| 133 | |
---|
[1093] | 134 | def drop_scan(self, scanid=None): |
---|
| 135 | """ |
---|
| 136 | Return a new scantable where the specified scan number(s) has(have) |
---|
| 137 | been dropped. |
---|
| 138 | Parameters: |
---|
| 139 | scanid: a (list of) scan number(s) |
---|
| 140 | """ |
---|
| 141 | from asap import _is_sequence_or_number as _is_valid |
---|
| 142 | from asap import _to_list |
---|
| 143 | from asap import unique |
---|
| 144 | if not _is_valid(scanid): |
---|
| 145 | if rcParams['verbose']: |
---|
| 146 | print "Please specify a scanno to drop from the scantable" |
---|
| 147 | return |
---|
| 148 | else: |
---|
| 149 | raise RuntimeError("No scan given") |
---|
| 150 | try: |
---|
| 151 | scanid = _to_list(scanid) |
---|
| 152 | allscans = unique([ self.getscan(i) for i in range(self.nrow())]) |
---|
| 153 | for sid in scanid: allscans.remove(sid) |
---|
[1118] | 154 | if len(allscans) == 0: |
---|
| 155 | raise ValueError("Can't remove all scans") |
---|
[1093] | 156 | except ValueError: |
---|
| 157 | if rcParams['verbose']: |
---|
| 158 | print "Couldn't find any match." |
---|
| 159 | return |
---|
| 160 | else: raise |
---|
| 161 | try: |
---|
| 162 | bsel = self.get_selection() |
---|
| 163 | sel = selector() |
---|
| 164 | sel.set_scans(allscans) |
---|
| 165 | self.set_selection(bsel+sel) |
---|
| 166 | scopy = self._copy() |
---|
| 167 | self.set_selection(bsel) |
---|
| 168 | return scantable(scopy) |
---|
| 169 | except RuntimeError: |
---|
[1118] | 170 | if rcParams['verbose']: |
---|
| 171 | print "Couldn't find any match." |
---|
| 172 | else: |
---|
| 173 | raise |
---|
[1093] | 174 | |
---|
| 175 | |
---|
[102] | 176 | def get_scan(self, scanid=None): |
---|
| 177 | """ |
---|
| 178 | Return a specific scan (by scanno) or collection of scans (by |
---|
| 179 | source name) in a new scantable. |
---|
| 180 | Parameters: |
---|
[513] | 181 | scanid: a (list of) scanno or a source name, unix-style |
---|
| 182 | patterns are accepted for source name matching, e.g. |
---|
| 183 | '*_R' gets all 'ref scans |
---|
[102] | 184 | Example: |
---|
[513] | 185 | # get all scans containing the source '323p459' |
---|
| 186 | newscan = scan.get_scan('323p459') |
---|
| 187 | # get all 'off' scans |
---|
| 188 | refscans = scan.get_scan('*_R') |
---|
| 189 | # get a susbset of scans by scanno (as listed in scan.summary()) |
---|
[1118] | 190 | newscan = scan.get_scan([0, 2, 7, 10]) |
---|
[102] | 191 | """ |
---|
| 192 | if scanid is None: |
---|
[718] | 193 | if rcParams['verbose']: |
---|
[1118] | 194 | print "Please specify a scan no or name to " \ |
---|
| 195 | "retrieve from the scantable" |
---|
[718] | 196 | return |
---|
| 197 | else: |
---|
| 198 | raise RuntimeError("No scan given") |
---|
| 199 | |
---|
[102] | 200 | try: |
---|
[946] | 201 | bsel = self.get_selection() |
---|
| 202 | sel = selector() |
---|
[102] | 203 | if type(scanid) is str: |
---|
[946] | 204 | sel.set_name(scanid) |
---|
| 205 | self.set_selection(bsel+sel) |
---|
[876] | 206 | scopy = self._copy() |
---|
[946] | 207 | self.set_selection(bsel) |
---|
[876] | 208 | return scantable(scopy) |
---|
[102] | 209 | elif type(scanid) is int: |
---|
[946] | 210 | sel.set_scans([scanid]) |
---|
| 211 | self.set_selection(bsel+sel) |
---|
[876] | 212 | scopy = self._copy() |
---|
[946] | 213 | self.set_selection(bsel) |
---|
[876] | 214 | return scantable(scopy) |
---|
[381] | 215 | elif type(scanid) is list: |
---|
[946] | 216 | sel.set_scans(scanid) |
---|
| 217 | self.set_selection(sel) |
---|
[876] | 218 | scopy = self._copy() |
---|
[946] | 219 | self.set_selection(bsel) |
---|
[876] | 220 | return scantable(scopy) |
---|
[381] | 221 | else: |
---|
[718] | 222 | msg = "Illegal scanid type, use 'int' or 'list' if ints." |
---|
| 223 | if rcParams['verbose']: |
---|
| 224 | print msg |
---|
| 225 | else: |
---|
| 226 | raise TypeError(msg) |
---|
[102] | 227 | except RuntimeError: |
---|
[718] | 228 | if rcParams['verbose']: print "Couldn't find any match." |
---|
| 229 | else: raise |
---|
[102] | 230 | |
---|
| 231 | def __str__(self): |
---|
[1118] | 232 | return Scantable._summary(self, True) |
---|
[102] | 233 | |
---|
[976] | 234 | def summary(self, filename=None): |
---|
[102] | 235 | """ |
---|
| 236 | Print a summary of the contents of this scantable. |
---|
| 237 | Parameters: |
---|
| 238 | filename: the name of a file to write the putput to |
---|
| 239 | Default - no file output |
---|
[381] | 240 | verbose: print extra info such as the frequency table |
---|
| 241 | The default (False) is taken from .asaprc |
---|
[102] | 242 | """ |
---|
[976] | 243 | info = Scantable._summary(self, True) |
---|
| 244 | #if verbose is None: verbose = rcParams['scantable.verbosesummary'] |
---|
[102] | 245 | if filename is not None: |
---|
[256] | 246 | if filename is "": |
---|
| 247 | filename = 'scantable_summary.txt' |
---|
[415] | 248 | from os.path import expandvars, isdir |
---|
[411] | 249 | filename = expandvars(filename) |
---|
[415] | 250 | if not isdir(filename): |
---|
[413] | 251 | data = open(filename, 'w') |
---|
| 252 | data.write(info) |
---|
| 253 | data.close() |
---|
| 254 | else: |
---|
[718] | 255 | msg = "Illegal file name '%s'." % (filename) |
---|
| 256 | if rcParams['verbose']: |
---|
| 257 | print msg |
---|
| 258 | else: |
---|
| 259 | raise IOError(msg) |
---|
| 260 | if rcParams['verbose']: |
---|
[794] | 261 | try: |
---|
| 262 | from IPython.genutils import page as pager |
---|
| 263 | except ImportError: |
---|
| 264 | from pydoc import pager |
---|
| 265 | pager(info) |
---|
[718] | 266 | else: |
---|
| 267 | return info |
---|
[710] | 268 | |
---|
[946] | 269 | |
---|
| 270 | def get_selection(self): |
---|
| 271 | """ |
---|
[1005] | 272 | Get the selection object currently set on this scantable. |
---|
| 273 | Parameters: |
---|
| 274 | none |
---|
| 275 | Example: |
---|
| 276 | sel = scan.get_selection() |
---|
| 277 | sel.set_ifs(0) # select IF 0 |
---|
| 278 | scan.set_selection(sel) # apply modified selection |
---|
[946] | 279 | """ |
---|
| 280 | return selector(self._getselection()) |
---|
| 281 | |
---|
[1005] | 282 | def set_selection(self, selection=selector()): |
---|
[946] | 283 | """ |
---|
[1005] | 284 | Select a subset of the data. All following operations on this scantable |
---|
| 285 | are only applied to thi selection. |
---|
| 286 | Parameters: |
---|
| 287 | selection: a selector object (default unset the selection) |
---|
| 288 | Examples: |
---|
| 289 | sel = selector() # create a selection object |
---|
[1118] | 290 | self.set_scans([0, 3]) # select SCANNO 0 and 3 |
---|
[1005] | 291 | scan.set_selection(sel) # set the selection |
---|
| 292 | scan.summary() # will only print summary of scanno 0 an 3 |
---|
| 293 | scan.set_selection() # unset the selection |
---|
[946] | 294 | """ |
---|
| 295 | self._setselection(selection) |
---|
| 296 | |
---|
[876] | 297 | def stats(self, stat='stddev', mask=None): |
---|
[102] | 298 | """ |
---|
[135] | 299 | Determine the specified statistic of the current beam/if/pol |
---|
[102] | 300 | Takes a 'mask' as an optional parameter to specify which |
---|
| 301 | channels should be excluded. |
---|
| 302 | Parameters: |
---|
[135] | 303 | stat: 'min', 'max', 'sumsq', 'sum', 'mean' |
---|
| 304 | 'var', 'stddev', 'avdev', 'rms', 'median' |
---|
| 305 | mask: an optional mask specifying where the statistic |
---|
[102] | 306 | should be determined. |
---|
| 307 | Example: |
---|
[113] | 308 | scan.set_unit('channel') |
---|
[1118] | 309 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 310 | scan.stats(stat='mean', mask=m) |
---|
[102] | 311 | """ |
---|
| 312 | if mask == None: |
---|
[876] | 313 | mask = [] |
---|
[1118] | 314 | axes = ['Beam', 'IF', 'Pol', 'Time'] |
---|
[876] | 315 | if not self._check_ifs(): |
---|
[1118] | 316 | raise ValueError("Cannot apply mask as the IFs have different " |
---|
| 317 | "number of channels. Please use setselection() " |
---|
| 318 | "to select individual IFs") |
---|
[256] | 319 | |
---|
[876] | 320 | statvals = self._math._stats(self, mask, stat) |
---|
| 321 | out = '' |
---|
| 322 | axes = [] |
---|
| 323 | for i in range(self.nrow()): |
---|
| 324 | axis = [] |
---|
| 325 | axis.append(self.getscan(i)) |
---|
| 326 | axis.append(self.getbeam(i)) |
---|
| 327 | axis.append(self.getif(i)) |
---|
| 328 | axis.append(self.getpol(i)) |
---|
| 329 | axis.append(self.getcycle(i)) |
---|
| 330 | axes.append(axis) |
---|
| 331 | tm = self._gettime(i) |
---|
| 332 | src = self._getsourcename(i) |
---|
| 333 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 334 | out += 'Time[%s]:\n' % (tm) |
---|
| 335 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 336 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 337 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 338 | out += '= %3.3f\n' % (statvals[i]) |
---|
| 339 | out += "--------------------------------------------------\n" |
---|
[256] | 340 | |
---|
[876] | 341 | if rcParams['verbose']: |
---|
| 342 | print "--------------------------------------------------" |
---|
[1118] | 343 | print " ", stat |
---|
[876] | 344 | print "--------------------------------------------------" |
---|
| 345 | print out |
---|
[1118] | 346 | retval = { 'axesnames': ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'], |
---|
[876] | 347 | 'axes' : axes, |
---|
| 348 | 'data': statvals} |
---|
| 349 | return retval |
---|
[102] | 350 | |
---|
[1118] | 351 | def stddev(self, mask=None): |
---|
[135] | 352 | """ |
---|
| 353 | Determine the standard deviation of the current beam/if/pol |
---|
| 354 | Takes a 'mask' as an optional parameter to specify which |
---|
| 355 | channels should be excluded. |
---|
| 356 | Parameters: |
---|
| 357 | mask: an optional mask specifying where the standard |
---|
| 358 | deviation should be determined. |
---|
| 359 | |
---|
| 360 | Example: |
---|
| 361 | scan.set_unit('channel') |
---|
[1118] | 362 | msk = scan.create_mask([100, 200], [500, 600]) |
---|
[135] | 363 | scan.stddev(mask=m) |
---|
| 364 | """ |
---|
[1118] | 365 | return self.stats(stat='stddev', mask=mask); |
---|
[135] | 366 | |
---|
[1003] | 367 | |
---|
| 368 | def column_names(self): |
---|
| 369 | """ |
---|
| 370 | Return a list of column names, which can be used for selection. |
---|
| 371 | """ |
---|
| 372 | return list(Scantable.column_names(self)) |
---|
| 373 | |
---|
[876] | 374 | def get_tsys(self): |
---|
[113] | 375 | """ |
---|
| 376 | Return the System temperatures. |
---|
| 377 | Parameters: |
---|
[876] | 378 | |
---|
[113] | 379 | Returns: |
---|
[876] | 380 | a list of Tsys values for the current selection |
---|
[113] | 381 | """ |
---|
[256] | 382 | |
---|
[876] | 383 | return self._row_callback(self._gettsys, "Tsys") |
---|
[256] | 384 | |
---|
[876] | 385 | def _row_callback(self, callback, label): |
---|
| 386 | axes = [] |
---|
[1118] | 387 | axesnames = ['scanno', 'beamno', 'ifno', 'polno', 'cycleno'] |
---|
[876] | 388 | out = "" |
---|
[1118] | 389 | outvec = [] |
---|
[876] | 390 | for i in range(self.nrow()): |
---|
| 391 | axis = [] |
---|
| 392 | axis.append(self.getscan(i)) |
---|
| 393 | axis.append(self.getbeam(i)) |
---|
| 394 | axis.append(self.getif(i)) |
---|
| 395 | axis.append(self.getpol(i)) |
---|
| 396 | axis.append(self.getcycle(i)) |
---|
| 397 | axes.append(axis) |
---|
| 398 | tm = self._gettime(i) |
---|
| 399 | src = self._getsourcename(i) |
---|
| 400 | out += 'Scan[%d] (%s) ' % (axis[0], src) |
---|
| 401 | out += 'Time[%s]:\n' % (tm) |
---|
| 402 | if self.nbeam(-1) > 1: out += ' Beam[%d] ' % (axis[1]) |
---|
| 403 | if self.nif(-1) > 1: out += ' IF[%d] ' % (axis[2]) |
---|
| 404 | if self.npol(-1) > 1: out += ' Pol[%d] ' % (axis[3]) |
---|
| 405 | outvec.append(callback(i)) |
---|
| 406 | out += '= %3.3f\n' % (outvec[i]) |
---|
| 407 | out += "--------------------------------------------------\n" |
---|
| 408 | if rcParams['verbose']: |
---|
| 409 | print "--------------------------------------------------" |
---|
| 410 | print " %s" % (label) |
---|
| 411 | print "--------------------------------------------------" |
---|
| 412 | print out |
---|
[1175] | 413 | # disabled because the vector seems more useful |
---|
| 414 | #retval = {'axesnames': axesnames, 'axes': axes, 'data': outvec} |
---|
| 415 | return outvec |
---|
[256] | 416 | |
---|
[1070] | 417 | def _get_column(self, callback, row=-1): |
---|
| 418 | """ |
---|
| 419 | """ |
---|
| 420 | if row == -1: |
---|
| 421 | return [callback(i) for i in range(self.nrow())] |
---|
| 422 | else: |
---|
| 423 | if 0 <= row < self.nrow(): |
---|
| 424 | return callback(row) |
---|
[256] | 425 | |
---|
[1070] | 426 | |
---|
[407] | 427 | def get_time(self, row=-1): |
---|
[113] | 428 | """ |
---|
| 429 | Get a list of time stamps for the observations. |
---|
[181] | 430 | Return a string for each integration in the scantable. |
---|
[113] | 431 | Parameters: |
---|
[407] | 432 | row: row no of integration. Default -1 return all rows |
---|
[113] | 433 | Example: |
---|
| 434 | none |
---|
| 435 | """ |
---|
[1175] | 436 | from time import strptime |
---|
| 437 | from datetime import datetime |
---|
| 438 | times = self._get_column(self._gettime, row) |
---|
| 439 | format = "%Y/%m/%d/%H:%M:%S" |
---|
| 440 | if isinstance(times, list): |
---|
| 441 | return [datetime(*strptime(i, format)[:6]) for i in times] |
---|
| 442 | else: |
---|
| 443 | return datetime(*strptime(times, format)[:6]) |
---|
[102] | 444 | |
---|
[714] | 445 | def get_sourcename(self, row=-1): |
---|
| 446 | """ |
---|
[794] | 447 | Get a list source names for the observations. |
---|
[714] | 448 | Return a string for each integration in the scantable. |
---|
| 449 | Parameters: |
---|
| 450 | row: row no of integration. Default -1 return all rows |
---|
| 451 | Example: |
---|
| 452 | none |
---|
| 453 | """ |
---|
[1070] | 454 | return self._get_column(self._getsourcename, row) |
---|
[714] | 455 | |
---|
[794] | 456 | def get_elevation(self, row=-1): |
---|
| 457 | """ |
---|
| 458 | Get a list of elevations for the observations. |
---|
| 459 | Return a float for each integration in the scantable. |
---|
| 460 | Parameters: |
---|
| 461 | row: row no of integration. Default -1 return all rows |
---|
| 462 | Example: |
---|
| 463 | none |
---|
| 464 | """ |
---|
[1070] | 465 | return self._get_column(self._getelevation, row) |
---|
[794] | 466 | |
---|
| 467 | def get_azimuth(self, row=-1): |
---|
| 468 | """ |
---|
| 469 | Get a list of azimuths for the observations. |
---|
| 470 | Return a float for each integration in the scantable. |
---|
| 471 | Parameters: |
---|
| 472 | row: row no of integration. Default -1 return all rows |
---|
| 473 | Example: |
---|
| 474 | none |
---|
| 475 | """ |
---|
[1070] | 476 | return self._get_column(self._getazimuth, row) |
---|
[794] | 477 | |
---|
| 478 | def get_parangle(self, row=-1): |
---|
| 479 | """ |
---|
| 480 | Get a list of parallactic angles for the observations. |
---|
| 481 | Return a float for each integration in the scantable. |
---|
| 482 | Parameters: |
---|
| 483 | row: row no of integration. Default -1 return all rows |
---|
| 484 | Example: |
---|
| 485 | none |
---|
| 486 | """ |
---|
[1070] | 487 | return self._get_column(self._getparangle, row) |
---|
[794] | 488 | |
---|
[1070] | 489 | def get_direction(self, row=-1): |
---|
| 490 | """ |
---|
| 491 | Get a list of Positions on the sky (direction) for the observations. |
---|
| 492 | Return a float for each integration in the scantable. |
---|
| 493 | Parameters: |
---|
| 494 | row: row no of integration. Default -1 return all rows |
---|
| 495 | Example: |
---|
| 496 | none |
---|
| 497 | """ |
---|
| 498 | return self._get_column(self._getdirection, row) |
---|
| 499 | |
---|
[102] | 500 | def set_unit(self, unit='channel'): |
---|
| 501 | """ |
---|
| 502 | Set the unit for all following operations on this scantable |
---|
| 503 | Parameters: |
---|
| 504 | unit: optional unit, default is 'channel' |
---|
[1118] | 505 | one of '*Hz', 'km/s', 'channel', '' |
---|
[102] | 506 | """ |
---|
[484] | 507 | varlist = vars() |
---|
[1118] | 508 | if unit in ['', 'pixel', 'channel']: |
---|
[113] | 509 | unit = '' |
---|
| 510 | inf = list(self._getcoordinfo()) |
---|
| 511 | inf[0] = unit |
---|
| 512 | self._setcoordinfo(inf) |
---|
[1118] | 513 | self._add_history("set_unit", varlist) |
---|
[113] | 514 | |
---|
[484] | 515 | def set_instrument(self, instr): |
---|
[358] | 516 | """ |
---|
| 517 | Set the instrument for subsequent processing |
---|
| 518 | Parameters: |
---|
[710] | 519 | instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', |
---|
[407] | 520 | 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' |
---|
[358] | 521 | """ |
---|
| 522 | self._setInstrument(instr) |
---|
[1118] | 523 | self._add_history("set_instument", vars()) |
---|
[718] | 524 | print_log() |
---|
[358] | 525 | |
---|
[276] | 526 | def set_doppler(self, doppler='RADIO'): |
---|
| 527 | """ |
---|
| 528 | Set the doppler for all following operations on this scantable. |
---|
| 529 | Parameters: |
---|
| 530 | doppler: One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA' |
---|
| 531 | """ |
---|
[484] | 532 | varlist = vars() |
---|
[276] | 533 | inf = list(self._getcoordinfo()) |
---|
| 534 | inf[2] = doppler |
---|
| 535 | self._setcoordinfo(inf) |
---|
[1118] | 536 | self._add_history("set_doppler", vars()) |
---|
[718] | 537 | print_log() |
---|
[710] | 538 | |
---|
[226] | 539 | def set_freqframe(self, frame=None): |
---|
[113] | 540 | """ |
---|
| 541 | Set the frame type of the Spectral Axis. |
---|
| 542 | Parameters: |
---|
[591] | 543 | frame: an optional frame type, default 'LSRK'. Valid frames are: |
---|
[1118] | 544 | 'REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', |
---|
| 545 | 'GEO', 'GALACTO', 'LGROUP', 'CMB' |
---|
[113] | 546 | Examples: |
---|
| 547 | scan.set_freqframe('BARY') |
---|
| 548 | """ |
---|
[484] | 549 | if frame is None: frame = rcParams['scantable.freqframe'] |
---|
| 550 | varlist = vars() |
---|
[1118] | 551 | valid = ['REST', 'TOPO', 'LSRD', 'LSRK', 'BARY', \ |
---|
| 552 | 'GEO', 'GALACTO', 'LGROUP', 'CMB'] |
---|
[591] | 553 | |
---|
[989] | 554 | if frame in valid: |
---|
[113] | 555 | inf = list(self._getcoordinfo()) |
---|
| 556 | inf[1] = frame |
---|
| 557 | self._setcoordinfo(inf) |
---|
[1118] | 558 | self._add_history("set_freqframe", varlist) |
---|
[102] | 559 | else: |
---|
[1118] | 560 | msg = "Please specify a valid freq type. Valid types are:\n", valid |
---|
[718] | 561 | if rcParams['verbose']: |
---|
| 562 | print msg |
---|
| 563 | else: |
---|
| 564 | raise TypeError(msg) |
---|
| 565 | print_log() |
---|
[710] | 566 | |
---|
[989] | 567 | def set_dirframe(self, frame=""): |
---|
| 568 | """ |
---|
| 569 | Set the frame type of the Direction on the sky. |
---|
| 570 | Parameters: |
---|
| 571 | frame: an optional frame type, default ''. Valid frames are: |
---|
| 572 | 'J2000', 'B1950', 'GALACTIC' |
---|
| 573 | Examples: |
---|
| 574 | scan.set_dirframe('GALACTIC') |
---|
| 575 | """ |
---|
| 576 | varlist = vars() |
---|
| 577 | try: |
---|
| 578 | Scantable.set_dirframe(self, frame) |
---|
[1118] | 579 | except RuntimeError, msg: |
---|
[989] | 580 | if rcParams['verbose']: |
---|
| 581 | print msg |
---|
| 582 | else: |
---|
| 583 | raise |
---|
[1118] | 584 | self._add_history("set_dirframe", varlist) |
---|
[989] | 585 | |
---|
[113] | 586 | def get_unit(self): |
---|
| 587 | """ |
---|
| 588 | Get the default unit set in this scantable |
---|
| 589 | Parameters: |
---|
| 590 | Returns: |
---|
| 591 | A unit string |
---|
| 592 | """ |
---|
| 593 | inf = self._getcoordinfo() |
---|
| 594 | unit = inf[0] |
---|
| 595 | if unit == '': unit = 'channel' |
---|
| 596 | return unit |
---|
[102] | 597 | |
---|
[158] | 598 | def get_abcissa(self, rowno=0): |
---|
[102] | 599 | """ |
---|
[158] | 600 | Get the abcissa in the current coordinate setup for the currently |
---|
[113] | 601 | selected Beam/IF/Pol |
---|
| 602 | Parameters: |
---|
[226] | 603 | rowno: an optional row number in the scantable. Default is the |
---|
| 604 | first row, i.e. rowno=0 |
---|
[113] | 605 | Returns: |
---|
[407] | 606 | The abcissa values and it's format string (as a dictionary) |
---|
[113] | 607 | """ |
---|
[256] | 608 | abc = self._getabcissa(rowno) |
---|
[710] | 609 | lbl = self._getabcissalabel(rowno) |
---|
[718] | 610 | print_log() |
---|
[158] | 611 | return abc, lbl |
---|
[113] | 612 | |
---|
[1118] | 613 | def flag(self, mask=None): |
---|
[1001] | 614 | """ |
---|
| 615 | Flag the selected data using an optional channel mask. |
---|
| 616 | Parameters: |
---|
| 617 | mask: an optional channel mask, created with create_mask. Default |
---|
| 618 | (no mask) is all channels. |
---|
| 619 | """ |
---|
| 620 | varlist = vars() |
---|
[1118] | 621 | if mask is None: |
---|
| 622 | mask = [] |
---|
[1001] | 623 | try: |
---|
| 624 | self._flag(mask) |
---|
[1118] | 625 | except RuntimeError, msg: |
---|
[1001] | 626 | if rcParams['verbose']: |
---|
| 627 | print msg |
---|
| 628 | return |
---|
| 629 | else: raise |
---|
| 630 | self._add_history("flag", varlist) |
---|
| 631 | |
---|
| 632 | |
---|
[113] | 633 | def create_mask(self, *args, **kwargs): |
---|
| 634 | """ |
---|
[1118] | 635 | Compute and return a mask based on [min, max] windows. |
---|
[189] | 636 | The specified windows are to be INCLUDED, when the mask is |
---|
[113] | 637 | applied. |
---|
[102] | 638 | Parameters: |
---|
[1118] | 639 | [min, max], [min2, max2], ... |
---|
[1024] | 640 | Pairs of start/end points (inclusive)specifying the regions |
---|
[102] | 641 | to be masked |
---|
[189] | 642 | invert: optional argument. If specified as True, |
---|
| 643 | return an inverted mask, i.e. the regions |
---|
| 644 | specified are EXCLUDED |
---|
[513] | 645 | row: create the mask using the specified row for |
---|
| 646 | unit conversions, default is row=0 |
---|
| 647 | only necessary if frequency varies over rows. |
---|
[102] | 648 | Example: |
---|
[113] | 649 | scan.set_unit('channel') |
---|
| 650 | a) |
---|
[1118] | 651 | msk = scan.create_mask([400, 500], [800, 900]) |
---|
[189] | 652 | # masks everything outside 400 and 500 |
---|
[113] | 653 | # and 800 and 900 in the unit 'channel' |
---|
| 654 | |
---|
| 655 | b) |
---|
[1118] | 656 | msk = scan.create_mask([400, 500], [800, 900], invert=True) |
---|
[189] | 657 | # masks the regions between 400 and 500 |
---|
[113] | 658 | # and 800 and 900 in the unit 'channel' |
---|
[1024] | 659 | c) |
---|
| 660 | mask only channel 400 |
---|
[1118] | 661 | msk = scan.create_mask([400, 400]) |
---|
[102] | 662 | """ |
---|
[513] | 663 | row = 0 |
---|
| 664 | if kwargs.has_key("row"): |
---|
| 665 | row = kwargs.get("row") |
---|
| 666 | data = self._getabcissa(row) |
---|
[113] | 667 | u = self._getcoordinfo()[0] |
---|
[718] | 668 | if rcParams['verbose']: |
---|
[113] | 669 | if u == "": u = "channel" |
---|
[718] | 670 | msg = "The current mask window unit is %s" % u |
---|
[1118] | 671 | i = self._check_ifs() |
---|
| 672 | if not i: |
---|
[876] | 673 | msg += "\nThis mask is only valid for IF=%d" % (self.getif(i)) |
---|
[718] | 674 | asaplog.push(msg) |
---|
[102] | 675 | n = self.nchan() |
---|
[1134] | 676 | msk = NUM.zeros(n) |
---|
[710] | 677 | # test if args is a 'list' or a 'normal *args - UGLY!!! |
---|
| 678 | |
---|
[1118] | 679 | ws = (isinstance(args[-1][-1], int) or isinstance(args[-1][-1], float)) \ |
---|
| 680 | and args or args[0] |
---|
[710] | 681 | for window in ws: |
---|
[102] | 682 | if (len(window) != 2 or window[0] > window[1] ): |
---|
[1118] | 683 | raise TypeError("A window needs to be defined as [min, max]") |
---|
[102] | 684 | for i in range(n): |
---|
[1024] | 685 | if data[i] >= window[0] and data[i] <= window[1]: |
---|
[189] | 686 | msk[i] = 1 |
---|
[113] | 687 | if kwargs.has_key('invert'): |
---|
| 688 | if kwargs.get('invert'): |
---|
[1134] | 689 | msk = NUM.logical_not(msk) |
---|
[718] | 690 | print_log() |
---|
[102] | 691 | return msk |
---|
[710] | 692 | |
---|
[256] | 693 | def get_restfreqs(self): |
---|
| 694 | """ |
---|
| 695 | Get the restfrequency(s) stored in this scantable. |
---|
| 696 | The return value(s) are always of unit 'Hz' |
---|
| 697 | Parameters: |
---|
| 698 | none |
---|
| 699 | Returns: |
---|
| 700 | a list of doubles |
---|
| 701 | """ |
---|
| 702 | return list(self._getrestfreqs()) |
---|
[102] | 703 | |
---|
[402] | 704 | |
---|
[931] | 705 | def set_restfreqs(self, freqs=None, unit='Hz'): |
---|
| 706 | """ |
---|
| 707 | Set or replace the restfrequency specified and |
---|
| 708 | If the 'freqs' argument holds a scalar, |
---|
| 709 | then that rest frequency will be applied to all the selected |
---|
| 710 | data. If the 'freqs' argument holds |
---|
| 711 | a vector, then it MUST be of equal or smaller length than |
---|
| 712 | the number of IFs (and the available restfrequencies will be |
---|
| 713 | replaced by this vector). In this case, *all* data have |
---|
| 714 | the restfrequency set per IF according |
---|
| 715 | to the corresponding value you give in the 'freqs' vector. |
---|
[1118] | 716 | E.g. 'freqs=[1e9, 2e9]' would mean IF 0 gets restfreq 1e9 and |
---|
[931] | 717 | IF 1 gets restfreq 2e9. |
---|
[1153] | 718 | You can also specify the frequencies via a linecatalog/ |
---|
| 719 | |
---|
[931] | 720 | Parameters: |
---|
| 721 | freqs: list of rest frequency values or string idenitfiers |
---|
| 722 | unit: unit for rest frequency (default 'Hz') |
---|
[402] | 723 | |
---|
[931] | 724 | Example: |
---|
| 725 | # set the given restfrequency for the whole table |
---|
| 726 | scan.set_restfreqs(freqs=1.4e9) |
---|
| 727 | # If thee number of IFs in the data is >= 2 the IF0 gets the first |
---|
| 728 | # value IF1 the second... |
---|
[1118] | 729 | scan.set_restfreqs(freqs=[1.4e9, 1.67e9]) |
---|
[931] | 730 | #set the given restfrequency for the whole table (by name) |
---|
| 731 | scan.set_restfreqs(freqs="OH1667") |
---|
[391] | 732 | |
---|
[931] | 733 | Note: |
---|
| 734 | To do more sophisticate Restfrequency setting, e.g. on a |
---|
| 735 | source and IF basis, use scantable.set_selection() before using |
---|
| 736 | this function. |
---|
| 737 | # provide your scantable is call scan |
---|
| 738 | selection = selector() |
---|
| 739 | selection.set_name("ORION*") |
---|
| 740 | selection.set_ifs([1]) |
---|
| 741 | scan.set_selection(selection) |
---|
| 742 | scan.set_restfreqs(freqs=86.6e9) |
---|
| 743 | |
---|
| 744 | """ |
---|
| 745 | varlist = vars() |
---|
[1157] | 746 | from asap import linecatalog |
---|
| 747 | # simple value |
---|
[1118] | 748 | if isinstance(freqs, int) or isinstance(freqs, float): |
---|
[1153] | 749 | self._setrestfreqs(freqs, "",unit) |
---|
[1157] | 750 | # list of values |
---|
[1118] | 751 | elif isinstance(freqs, list) or isinstance(freqs, tuple): |
---|
[1157] | 752 | # list values are scalars |
---|
[1118] | 753 | if isinstance(freqs[-1], int) or isinstance(freqs[-1], float): |
---|
[931] | 754 | sel = selector() |
---|
| 755 | savesel = self._getselection() |
---|
| 756 | for i in xrange(len(freqs)): |
---|
[946] | 757 | sel.set_ifs([i]) |
---|
[931] | 758 | self._setselection(sel) |
---|
[1153] | 759 | self._setrestfreqs(freqs[i], "",unit) |
---|
[931] | 760 | self._setselection(savesel) |
---|
[1157] | 761 | # list values are tuples, (value, name) |
---|
| 762 | elif isinstance(freqs[-1], dict): |
---|
| 763 | sel = selector() |
---|
| 764 | savesel = self._getselection() |
---|
| 765 | for i in xrange(len(freqs)): |
---|
| 766 | sel.set_ifs([i]) |
---|
| 767 | self._setrestfreqs(freqs[i]["value"], |
---|
| 768 | freqs[i]["name"], "MHz") |
---|
| 769 | self._setselection(sel) |
---|
| 770 | self._setselection(savesel) |
---|
| 771 | # freqs are to be taken from a linecatalog |
---|
[1153] | 772 | elif isinstance(freqs, linecatalog): |
---|
| 773 | sel = selector() |
---|
| 774 | savesel = self._getselection() |
---|
| 775 | for i in xrange(freqs.nrow()): |
---|
| 776 | sel.set_ifs([i]) |
---|
| 777 | self._setselection(sel) |
---|
| 778 | self._setrestfreqs(freqs.get_frequency(i), |
---|
| 779 | freqs.get_name(i), "MHz") |
---|
| 780 | # ensure that we are not iterating past nIF |
---|
| 781 | if i == self.nif()-1: break |
---|
| 782 | self._setselection(savesel) |
---|
[931] | 783 | else: |
---|
| 784 | return |
---|
| 785 | self._add_history("set_restfreqs", varlist) |
---|
| 786 | |
---|
| 787 | |
---|
| 788 | |
---|
[484] | 789 | def history(self): |
---|
| 790 | hist = list(self._gethistory()) |
---|
[794] | 791 | out = "-"*80 |
---|
[484] | 792 | for h in hist: |
---|
[489] | 793 | if h.startswith("---"): |
---|
[794] | 794 | out += "\n"+h |
---|
[489] | 795 | else: |
---|
| 796 | items = h.split("##") |
---|
| 797 | date = items[0] |
---|
| 798 | func = items[1] |
---|
| 799 | items = items[2:] |
---|
[794] | 800 | out += "\n"+date+"\n" |
---|
| 801 | out += "Function: %s\n Parameters:" % (func) |
---|
[489] | 802 | for i in items: |
---|
| 803 | s = i.split("=") |
---|
[1118] | 804 | out += "\n %s = %s" % (s[0], s[1]) |
---|
[794] | 805 | out += "\n"+"-"*80 |
---|
| 806 | try: |
---|
| 807 | from IPython.genutils import page as pager |
---|
| 808 | except ImportError: |
---|
| 809 | from pydoc import pager |
---|
| 810 | pager(out) |
---|
[484] | 811 | return |
---|
| 812 | |
---|
[513] | 813 | # |
---|
| 814 | # Maths business |
---|
| 815 | # |
---|
| 816 | |
---|
[931] | 817 | def average_time(self, mask=None, scanav=False, weight='tint', align=False): |
---|
[513] | 818 | """ |
---|
[1070] | 819 | Return the (time) weighted average of a scan. |
---|
[513] | 820 | Note: |
---|
[1070] | 821 | in channels only - align if necessary |
---|
[513] | 822 | Parameters: |
---|
| 823 | mask: an optional mask (only used for 'var' and 'tsys' |
---|
| 824 | weighting) |
---|
[558] | 825 | scanav: True averages each scan separately |
---|
| 826 | False (default) averages all scans together, |
---|
[1099] | 827 | weight: Weighting scheme. |
---|
| 828 | 'none' (mean no weight) |
---|
| 829 | 'var' (1/var(spec) weighted) |
---|
| 830 | 'tsys' (1/Tsys**2 weighted) |
---|
| 831 | 'tint' (integration time weighted) |
---|
| 832 | 'tintsys' (Tint/Tsys**2) |
---|
| 833 | 'median' ( median averaging) |
---|
[535] | 834 | The default is 'tint' |
---|
[931] | 835 | align: align the spectra in velocity before averaging. It takes |
---|
| 836 | the time of the first spectrum as reference time. |
---|
[513] | 837 | Example: |
---|
| 838 | # time average the scantable without using a mask |
---|
[710] | 839 | newscan = scan.average_time() |
---|
[513] | 840 | """ |
---|
| 841 | varlist = vars() |
---|
[976] | 842 | if weight is None: weight = 'TINT' |
---|
[513] | 843 | if mask is None: mask = () |
---|
[1099] | 844 | if scanav: scanav = "SCAN" |
---|
| 845 | else: scanav = "NONE" |
---|
[1118] | 846 | scan = (self, ) |
---|
[989] | 847 | try: |
---|
[1118] | 848 | if align: |
---|
| 849 | scan = (self.freq_align(insitu=False), ) |
---|
| 850 | s = None |
---|
| 851 | if weight.upper() == 'MEDIAN': |
---|
| 852 | s = scantable(self._math._averagechannel(scan[0], 'MEDIAN', |
---|
| 853 | scanav)) |
---|
| 854 | else: |
---|
| 855 | s = scantable(self._math._average(scan, mask, weight.upper(), |
---|
| 856 | scanav)) |
---|
| 857 | except RuntimeError, msg: |
---|
[989] | 858 | if rcParams['verbose']: |
---|
| 859 | print msg |
---|
| 860 | return |
---|
| 861 | else: raise |
---|
[1099] | 862 | s._add_history("average_time", varlist) |
---|
[718] | 863 | print_log() |
---|
[513] | 864 | return s |
---|
[710] | 865 | |
---|
[876] | 866 | def convert_flux(self, jyperk=None, eta=None, d=None, insitu=None): |
---|
[513] | 867 | """ |
---|
| 868 | Return a scan where all spectra are converted to either |
---|
| 869 | Jansky or Kelvin depending upon the flux units of the scan table. |
---|
| 870 | By default the function tries to look the values up internally. |
---|
| 871 | If it can't find them (or if you want to over-ride), you must |
---|
| 872 | specify EITHER jyperk OR eta (and D which it will try to look up |
---|
| 873 | also if you don't set it). jyperk takes precedence if you set both. |
---|
| 874 | Parameters: |
---|
| 875 | jyperk: the Jy / K conversion factor |
---|
| 876 | eta: the aperture efficiency |
---|
| 877 | d: the geomtric diameter (metres) |
---|
| 878 | insitu: if False a new scantable is returned. |
---|
| 879 | Otherwise, the scaling is done in-situ |
---|
| 880 | The default is taken from .asaprc (False) |
---|
| 881 | allaxes: if True apply to all spectra. Otherwise |
---|
| 882 | apply only to the selected (beam/pol/if)spectra only |
---|
| 883 | The default is taken from .asaprc (True if none) |
---|
| 884 | """ |
---|
| 885 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 886 | self._math._setinsitu(insitu) |
---|
[513] | 887 | varlist = vars() |
---|
| 888 | if jyperk is None: jyperk = -1.0 |
---|
| 889 | if d is None: d = -1.0 |
---|
| 890 | if eta is None: eta = -1.0 |
---|
[876] | 891 | s = scantable(self._math._convertflux(self, d, eta, jyperk)) |
---|
| 892 | s._add_history("convert_flux", varlist) |
---|
| 893 | print_log() |
---|
| 894 | if insitu: self._assign(s) |
---|
| 895 | else: return s |
---|
[513] | 896 | |
---|
[876] | 897 | def gain_el(self, poly=None, filename="", method="linear", insitu=None): |
---|
[513] | 898 | """ |
---|
| 899 | Return a scan after applying a gain-elevation correction. |
---|
| 900 | The correction can be made via either a polynomial or a |
---|
| 901 | table-based interpolation (and extrapolation if necessary). |
---|
| 902 | You specify polynomial coefficients, an ascii table or neither. |
---|
| 903 | If you specify neither, then a polynomial correction will be made |
---|
| 904 | with built in coefficients known for certain telescopes (an error |
---|
| 905 | will occur if the instrument is not known). |
---|
| 906 | The data and Tsys are *divided* by the scaling factors. |
---|
| 907 | Parameters: |
---|
| 908 | poly: Polynomial coefficients (default None) to compute a |
---|
| 909 | gain-elevation correction as a function of |
---|
| 910 | elevation (in degrees). |
---|
| 911 | filename: The name of an ascii file holding correction factors. |
---|
| 912 | The first row of the ascii file must give the column |
---|
| 913 | names and these MUST include columns |
---|
| 914 | "ELEVATION" (degrees) and "FACTOR" (multiply data |
---|
| 915 | by this) somewhere. |
---|
| 916 | The second row must give the data type of the |
---|
| 917 | column. Use 'R' for Real and 'I' for Integer. |
---|
| 918 | An example file would be |
---|
| 919 | (actual factors are arbitrary) : |
---|
| 920 | |
---|
| 921 | TIME ELEVATION FACTOR |
---|
| 922 | R R R |
---|
| 923 | 0.1 0 0.8 |
---|
| 924 | 0.2 20 0.85 |
---|
| 925 | 0.3 40 0.9 |
---|
| 926 | 0.4 60 0.85 |
---|
| 927 | 0.5 80 0.8 |
---|
| 928 | 0.6 90 0.75 |
---|
| 929 | method: Interpolation method when correcting from a table. |
---|
| 930 | Values are "nearest", "linear" (default), "cubic" |
---|
| 931 | and "spline" |
---|
| 932 | insitu: if False a new scantable is returned. |
---|
| 933 | Otherwise, the scaling is done in-situ |
---|
| 934 | The default is taken from .asaprc (False) |
---|
| 935 | """ |
---|
| 936 | |
---|
| 937 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 938 | self._math._setinsitu(insitu) |
---|
[513] | 939 | varlist = vars() |
---|
| 940 | if poly is None: |
---|
[1118] | 941 | poly = () |
---|
[513] | 942 | from os.path import expandvars |
---|
| 943 | filename = expandvars(filename) |
---|
[876] | 944 | s = scantable(self._math._gainel(self, poly, filename, method)) |
---|
| 945 | s._add_history("gain_el", varlist) |
---|
| 946 | print_log() |
---|
| 947 | if insitu: self._assign(s) |
---|
| 948 | else: return s |
---|
[710] | 949 | |
---|
[931] | 950 | def freq_align(self, reftime=None, method='cubic', insitu=None): |
---|
[513] | 951 | """ |
---|
| 952 | Return a scan where all rows have been aligned in frequency/velocity. |
---|
| 953 | The alignment frequency frame (e.g. LSRK) is that set by function |
---|
| 954 | set_freqframe. |
---|
| 955 | Parameters: |
---|
| 956 | reftime: reference time to align at. By default, the time of |
---|
| 957 | the first row of data is used. |
---|
| 958 | method: Interpolation method for regridding the spectra. |
---|
| 959 | Choose from "nearest", "linear", "cubic" (default) |
---|
| 960 | and "spline" |
---|
| 961 | insitu: if False a new scantable is returned. |
---|
| 962 | Otherwise, the scaling is done in-situ |
---|
| 963 | The default is taken from .asaprc (False) |
---|
| 964 | """ |
---|
[931] | 965 | if insitu is None: insitu = rcParams["insitu"] |
---|
[876] | 966 | self._math._setinsitu(insitu) |
---|
[513] | 967 | varlist = vars() |
---|
[931] | 968 | if reftime is None: reftime = "" |
---|
| 969 | s = scantable(self._math._freq_align(self, reftime, method)) |
---|
[876] | 970 | s._add_history("freq_align", varlist) |
---|
| 971 | print_log() |
---|
| 972 | if insitu: self._assign(s) |
---|
| 973 | else: return s |
---|
[513] | 974 | |
---|
[876] | 975 | def opacity(self, tau, insitu=None): |
---|
[513] | 976 | """ |
---|
| 977 | Apply an opacity correction. The data |
---|
| 978 | and Tsys are multiplied by the correction factor. |
---|
| 979 | Parameters: |
---|
| 980 | tau: Opacity from which the correction factor is |
---|
| 981 | exp(tau*ZD) |
---|
| 982 | where ZD is the zenith-distance |
---|
| 983 | insitu: if False a new scantable is returned. |
---|
| 984 | Otherwise, the scaling is done in-situ |
---|
| 985 | The default is taken from .asaprc (False) |
---|
| 986 | """ |
---|
| 987 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 988 | self._math._setinsitu(insitu) |
---|
[513] | 989 | varlist = vars() |
---|
[876] | 990 | s = scantable(self._math._opacity(self, tau)) |
---|
| 991 | s._add_history("opacity", varlist) |
---|
| 992 | print_log() |
---|
| 993 | if insitu: self._assign(s) |
---|
| 994 | else: return s |
---|
[513] | 995 | |
---|
| 996 | def bin(self, width=5, insitu=None): |
---|
| 997 | """ |
---|
| 998 | Return a scan where all spectra have been binned up. |
---|
| 999 | width: The bin width (default=5) in pixels |
---|
| 1000 | insitu: if False a new scantable is returned. |
---|
| 1001 | Otherwise, the scaling is done in-situ |
---|
| 1002 | The default is taken from .asaprc (False) |
---|
| 1003 | """ |
---|
| 1004 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1005 | self._math._setinsitu(insitu) |
---|
[513] | 1006 | varlist = vars() |
---|
[876] | 1007 | s = scantable(self._math._bin(self, width)) |
---|
[1118] | 1008 | s._add_history("bin", varlist) |
---|
[876] | 1009 | print_log() |
---|
| 1010 | if insitu: self._assign(s) |
---|
| 1011 | else: return s |
---|
[513] | 1012 | |
---|
[710] | 1013 | |
---|
[513] | 1014 | def resample(self, width=5, method='cubic', insitu=None): |
---|
| 1015 | """ |
---|
| 1016 | Return a scan where all spectra have been binned up |
---|
| 1017 | width: The bin width (default=5) in pixels |
---|
| 1018 | method: Interpolation method when correcting from a table. |
---|
| 1019 | Values are "nearest", "linear", "cubic" (default) |
---|
| 1020 | and "spline" |
---|
| 1021 | insitu: if False a new scantable is returned. |
---|
| 1022 | Otherwise, the scaling is done in-situ |
---|
| 1023 | The default is taken from .asaprc (False) |
---|
| 1024 | """ |
---|
| 1025 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1026 | self._math._setinsitu(insitu) |
---|
[513] | 1027 | varlist = vars() |
---|
[876] | 1028 | s = scantable(self._math._resample(self, method, width)) |
---|
[1118] | 1029 | s._add_history("resample", varlist) |
---|
[876] | 1030 | print_log() |
---|
| 1031 | if insitu: self._assign(s) |
---|
| 1032 | else: return s |
---|
[513] | 1033 | |
---|
| 1034 | |
---|
[946] | 1035 | def average_pol(self, mask=None, weight='none'): |
---|
| 1036 | """ |
---|
| 1037 | Average the Polarisations together. |
---|
| 1038 | Parameters: |
---|
| 1039 | mask: An optional mask defining the region, where the |
---|
| 1040 | averaging will be applied. The output will have all |
---|
| 1041 | specified points masked. |
---|
| 1042 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1043 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1044 | """ |
---|
| 1045 | varlist = vars() |
---|
| 1046 | if mask is None: |
---|
| 1047 | mask = () |
---|
[1010] | 1048 | s = scantable(self._math._averagepol(self, mask, weight.upper())) |
---|
[1118] | 1049 | s._add_history("average_pol", varlist) |
---|
[946] | 1050 | print_log() |
---|
[992] | 1051 | return s |
---|
[513] | 1052 | |
---|
[1145] | 1053 | def average_beam(self, mask=None, weight='none'): |
---|
| 1054 | """ |
---|
| 1055 | Average the Beams together. |
---|
| 1056 | Parameters: |
---|
| 1057 | mask: An optional mask defining the region, where the |
---|
| 1058 | averaging will be applied. The output will have all |
---|
| 1059 | specified points masked. |
---|
| 1060 | weight: Weighting scheme. 'none' (default), 'var' (1/var(spec) |
---|
| 1061 | weighted), or 'tsys' (1/Tsys**2 weighted) |
---|
| 1062 | """ |
---|
| 1063 | varlist = vars() |
---|
| 1064 | if mask is None: |
---|
| 1065 | mask = () |
---|
| 1066 | s = scantable(self._math._averagebeams(self, mask, weight.upper())) |
---|
| 1067 | s._add_history("average_beam", varlist) |
---|
| 1068 | print_log() |
---|
| 1069 | return s |
---|
| 1070 | |
---|
[992] | 1071 | def convert_pol(self, poltype=None): |
---|
| 1072 | """ |
---|
| 1073 | Convert the data to a different polarisation type. |
---|
| 1074 | Parameters: |
---|
| 1075 | poltype: The new polarisation type. Valid types are: |
---|
| 1076 | "linear", "stokes" and "circular" |
---|
| 1077 | """ |
---|
| 1078 | varlist = vars() |
---|
| 1079 | try: |
---|
| 1080 | s = scantable(self._math._convertpol(self, poltype)) |
---|
[1118] | 1081 | except RuntimeError, msg: |
---|
[992] | 1082 | if rcParams['verbose']: |
---|
[1118] | 1083 | print msg |
---|
| 1084 | return |
---|
[992] | 1085 | else: |
---|
| 1086 | raise |
---|
[1118] | 1087 | s._add_history("convert_pol", varlist) |
---|
[992] | 1088 | print_log() |
---|
| 1089 | return s |
---|
| 1090 | |
---|
[876] | 1091 | def smooth(self, kernel="hanning", width=5.0, insitu=None): |
---|
[513] | 1092 | """ |
---|
| 1093 | Smooth the spectrum by the specified kernel (conserving flux). |
---|
| 1094 | Parameters: |
---|
| 1095 | scan: The input scan |
---|
| 1096 | kernel: The type of smoothing kernel. Select from |
---|
| 1097 | 'hanning' (default), 'gaussian' and 'boxcar'. |
---|
| 1098 | The first three characters are sufficient. |
---|
| 1099 | width: The width of the kernel in pixels. For hanning this is |
---|
| 1100 | ignored otherwise it defauls to 5 pixels. |
---|
| 1101 | For 'gaussian' it is the Full Width Half |
---|
| 1102 | Maximum. For 'boxcar' it is the full width. |
---|
| 1103 | insitu: if False a new scantable is returned. |
---|
| 1104 | Otherwise, the scaling is done in-situ |
---|
| 1105 | The default is taken from .asaprc (False) |
---|
| 1106 | Example: |
---|
| 1107 | none |
---|
| 1108 | """ |
---|
| 1109 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1110 | self._math._setinsitu(insitu) |
---|
[513] | 1111 | varlist = vars() |
---|
[1118] | 1112 | s = scantable(self._math._smooth(self, kernel.lower(), width)) |
---|
[876] | 1113 | s._add_history("smooth", varlist) |
---|
| 1114 | print_log() |
---|
| 1115 | if insitu: self._assign(s) |
---|
| 1116 | else: return s |
---|
[513] | 1117 | |
---|
[876] | 1118 | |
---|
[1061] | 1119 | def poly_baseline(self, mask=None, order=0, plot=False, insitu=None): |
---|
[513] | 1120 | """ |
---|
| 1121 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1122 | Parameters: |
---|
[794] | 1123 | scan: a scantable |
---|
| 1124 | mask: an optional mask |
---|
| 1125 | order: the order of the polynomial (default is 0) |
---|
[1061] | 1126 | plot: plot the fit and the residual. In this each |
---|
| 1127 | indivual fit has to be approved, by typing 'y' |
---|
| 1128 | or 'n' |
---|
[794] | 1129 | insitu: if False a new scantable is returned. |
---|
| 1130 | Otherwise, the scaling is done in-situ |
---|
| 1131 | The default is taken from .asaprc (False) |
---|
[513] | 1132 | Example: |
---|
| 1133 | # return a scan baselined by a third order polynomial, |
---|
| 1134 | # not using a mask |
---|
| 1135 | bscan = scan.poly_baseline(order=3) |
---|
[579] | 1136 | """ |
---|
[513] | 1137 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1138 | varlist = vars() |
---|
| 1139 | if mask is None: |
---|
[1134] | 1140 | mask = list(NUM.ones(self.nchan(-1))) |
---|
[513] | 1141 | from asap.asapfitter import fitter |
---|
| 1142 | f = fitter() |
---|
| 1143 | f.set_scan(self, mask) |
---|
| 1144 | f.set_function(poly=order) |
---|
[1061] | 1145 | s = f.auto_fit(insitu, plot=plot) |
---|
[876] | 1146 | s._add_history("poly_baseline", varlist) |
---|
[718] | 1147 | print_log() |
---|
[876] | 1148 | if insitu: self._assign(s) |
---|
| 1149 | else: return s |
---|
[513] | 1150 | |
---|
[1118] | 1151 | def auto_poly_baseline(self, mask=[], edge=(0, 0), order=0, |
---|
[1061] | 1152 | threshold=3, plot=False, insitu=None): |
---|
[880] | 1153 | """ |
---|
| 1154 | Return a scan which has been baselined (all rows) by a polynomial. |
---|
| 1155 | Spectral lines are detected first using linefinder and masked out |
---|
| 1156 | to avoid them affecting the baseline solution. |
---|
| 1157 | |
---|
| 1158 | Parameters: |
---|
| 1159 | mask: an optional mask retreived from scantable |
---|
| 1160 | edge: an optional number of channel to drop at |
---|
| 1161 | the edge of spectrum. If only one value is |
---|
| 1162 | specified, the same number will be dropped from |
---|
| 1163 | both sides of the spectrum. Default is to keep |
---|
[907] | 1164 | all channels. Nested tuples represent individual |
---|
[976] | 1165 | edge selection for different IFs (a number of spectral |
---|
| 1166 | channels can be different) |
---|
[880] | 1167 | order: the order of the polynomial (default is 0) |
---|
| 1168 | threshold: the threshold used by line finder. It is better to |
---|
| 1169 | keep it large as only strong lines affect the |
---|
| 1170 | baseline solution. |
---|
[1061] | 1171 | plot: plot the fit and the residual. In this each |
---|
| 1172 | indivual fit has to be approved, by typing 'y' |
---|
| 1173 | or 'n' |
---|
[880] | 1174 | insitu: if False a new scantable is returned. |
---|
| 1175 | Otherwise, the scaling is done in-situ |
---|
| 1176 | The default is taken from .asaprc (False) |
---|
| 1177 | |
---|
| 1178 | Example: |
---|
| 1179 | scan2=scan.auto_poly_baseline(order=7) |
---|
| 1180 | """ |
---|
| 1181 | if insitu is None: insitu = rcParams['insitu'] |
---|
| 1182 | varlist = vars() |
---|
| 1183 | from asap.asapfitter import fitter |
---|
| 1184 | from asap.asaplinefind import linefinder |
---|
| 1185 | from asap import _is_sequence_or_number as _is_valid |
---|
| 1186 | |
---|
[976] | 1187 | # check whether edge is set up for each IF individually |
---|
[1118] | 1188 | individualedge = False; |
---|
| 1189 | if len(edge) > 1: |
---|
| 1190 | if isinstance(edge[0], list) or isinstance(edge[0], tuple): |
---|
| 1191 | individualedge = True; |
---|
[907] | 1192 | |
---|
[1118] | 1193 | if not _is_valid(edge, int) and not individualedge: |
---|
[909] | 1194 | raise ValueError, "Parameter 'edge' has to be an integer or a \ |
---|
[907] | 1195 | pair of integers specified as a tuple. Nested tuples are allowed \ |
---|
| 1196 | to make individual selection for different IFs." |
---|
[919] | 1197 | |
---|
[1118] | 1198 | curedge = (0, 0) |
---|
| 1199 | if individualedge: |
---|
| 1200 | for edgepar in edge: |
---|
| 1201 | if not _is_valid(edgepar, int): |
---|
| 1202 | raise ValueError, "Each element of the 'edge' tuple has \ |
---|
| 1203 | to be a pair of integers or an integer." |
---|
[907] | 1204 | else: |
---|
[1118] | 1205 | curedge = edge; |
---|
[880] | 1206 | |
---|
| 1207 | # setup fitter |
---|
| 1208 | f = fitter() |
---|
| 1209 | f.set_function(poly=order) |
---|
| 1210 | |
---|
| 1211 | # setup line finder |
---|
[1118] | 1212 | fl = linefinder() |
---|
[880] | 1213 | fl.set_options(threshold=threshold) |
---|
| 1214 | |
---|
| 1215 | if not insitu: |
---|
[1118] | 1216 | workscan = self.copy() |
---|
[880] | 1217 | else: |
---|
[1118] | 1218 | workscan = self |
---|
[880] | 1219 | |
---|
[907] | 1220 | fl.set_scan(workscan) |
---|
| 1221 | |
---|
[1118] | 1222 | rows = range(workscan.nrow()) |
---|
[880] | 1223 | asaplog.push("Processing:") |
---|
| 1224 | for r in rows: |
---|
[1118] | 1225 | msg = " Scan[%d] Beam[%d] IF[%d] Pol[%d] Cycle[%d]" % \ |
---|
| 1226 | (workscan.getscan(r), workscan.getbeam(r), workscan.getif(r), \ |
---|
| 1227 | workscan.getpol(r), workscan.getcycle(r)) |
---|
[880] | 1228 | asaplog.push(msg, False) |
---|
[907] | 1229 | |
---|
[976] | 1230 | # figure out edge parameter |
---|
[1118] | 1231 | if individualedge: |
---|
| 1232 | if len(edge) >= workscan.getif(r): |
---|
| 1233 | raise RuntimeError, "Number of edge elements appear to " \ |
---|
| 1234 | "be less than the number of IFs" |
---|
| 1235 | curedge = edge[workscan.getif(r)] |
---|
[919] | 1236 | |
---|
[976] | 1237 | # setup line finder |
---|
[1118] | 1238 | fl.find_lines(r, mask, curedge) |
---|
[880] | 1239 | f.set_scan(workscan, fl.get_mask()) |
---|
| 1240 | f.x = workscan._getabcissa(r) |
---|
| 1241 | f.y = workscan._getspectrum(r) |
---|
| 1242 | f.data = None |
---|
| 1243 | f.fit() |
---|
| 1244 | x = f.get_parameters() |
---|
[1061] | 1245 | if plot: |
---|
| 1246 | f.plot(residual=True) |
---|
| 1247 | x = raw_input("Accept fit ( [y]/n ): ") |
---|
| 1248 | if x.upper() == 'N': |
---|
| 1249 | continue |
---|
[880] | 1250 | workscan._setspectrum(f.fitter.getresidual(), r) |
---|
[1061] | 1251 | if plot: |
---|
| 1252 | f._p.unmap() |
---|
| 1253 | f._p = None |
---|
| 1254 | workscan._add_history("auto_poly_baseline", varlist) |
---|
[880] | 1255 | if insitu: |
---|
| 1256 | self._assign(workscan) |
---|
| 1257 | else: |
---|
| 1258 | return workscan |
---|
| 1259 | |
---|
[914] | 1260 | def rotate_linpolphase(self, angle): |
---|
| 1261 | """ |
---|
| 1262 | Rotate the phase of the complex polarization O=Q+iU correlation. |
---|
| 1263 | This is always done in situ in the raw data. So if you call this |
---|
| 1264 | function more than once then each call rotates the phase further. |
---|
| 1265 | Parameters: |
---|
| 1266 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1267 | Examples: |
---|
| 1268 | scan.rotate_linpolphase(2.3) |
---|
| 1269 | """ |
---|
| 1270 | varlist = vars() |
---|
[936] | 1271 | self._math._rotate_linpolphase(self, angle) |
---|
[914] | 1272 | self._add_history("rotate_linpolphase", varlist) |
---|
| 1273 | print_log() |
---|
| 1274 | return |
---|
[710] | 1275 | |
---|
[513] | 1276 | |
---|
[914] | 1277 | def rotate_xyphase(self, angle): |
---|
| 1278 | """ |
---|
| 1279 | Rotate the phase of the XY correlation. This is always done in situ |
---|
| 1280 | in the data. So if you call this function more than once |
---|
| 1281 | then each call rotates the phase further. |
---|
| 1282 | Parameters: |
---|
| 1283 | angle: The angle (degrees) to rotate (add) by. |
---|
| 1284 | Examples: |
---|
| 1285 | scan.rotate_xyphase(2.3) |
---|
| 1286 | """ |
---|
| 1287 | varlist = vars() |
---|
[936] | 1288 | self._math._rotate_xyphase(self, angle) |
---|
[914] | 1289 | self._add_history("rotate_xyphase", varlist) |
---|
| 1290 | print_log() |
---|
| 1291 | return |
---|
| 1292 | |
---|
| 1293 | def swap_linears(self): |
---|
| 1294 | """ |
---|
| 1295 | Swap the linear polarisations XX and YY |
---|
| 1296 | """ |
---|
| 1297 | varlist = vars() |
---|
[936] | 1298 | self._math._swap_linears(self) |
---|
[914] | 1299 | self._add_history("swap_linears", varlist) |
---|
| 1300 | print_log() |
---|
| 1301 | return |
---|
| 1302 | |
---|
| 1303 | def invert_phase(self): |
---|
| 1304 | """ |
---|
| 1305 | Invert the phase of the complex polarisation |
---|
| 1306 | """ |
---|
| 1307 | varlist = vars() |
---|
[936] | 1308 | self._math._invert_phase(self) |
---|
[914] | 1309 | self._add_history("invert_phase", varlist) |
---|
| 1310 | print_log() |
---|
| 1311 | return |
---|
| 1312 | |
---|
[876] | 1313 | def add(self, offset, insitu=None): |
---|
[513] | 1314 | """ |
---|
| 1315 | Return a scan where all spectra have the offset added |
---|
| 1316 | Parameters: |
---|
| 1317 | offset: the offset |
---|
| 1318 | insitu: if False a new scantable is returned. |
---|
| 1319 | Otherwise, the scaling is done in-situ |
---|
| 1320 | The default is taken from .asaprc (False) |
---|
| 1321 | """ |
---|
| 1322 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1323 | self._math._setinsitu(insitu) |
---|
[513] | 1324 | varlist = vars() |
---|
[876] | 1325 | s = scantable(self._math._unaryop(self, offset, "ADD", False)) |
---|
[1118] | 1326 | s._add_history("add", varlist) |
---|
[876] | 1327 | print_log() |
---|
| 1328 | if insitu: |
---|
| 1329 | self._assign(s) |
---|
| 1330 | else: |
---|
[513] | 1331 | return s |
---|
| 1332 | |
---|
[1118] | 1333 | def scale(self, factor, tsys=True, insitu=None, ): |
---|
[513] | 1334 | """ |
---|
| 1335 | Return a scan where all spectra are scaled by the give 'factor' |
---|
| 1336 | Parameters: |
---|
| 1337 | factor: the scaling factor |
---|
| 1338 | insitu: if False a new scantable is returned. |
---|
| 1339 | Otherwise, the scaling is done in-situ |
---|
| 1340 | The default is taken from .asaprc (False) |
---|
| 1341 | tsys: if True (default) then apply the operation to Tsys |
---|
| 1342 | as well as the data |
---|
| 1343 | """ |
---|
| 1344 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1345 | self._math._setinsitu(insitu) |
---|
[513] | 1346 | varlist = vars() |
---|
[876] | 1347 | s = scantable(self._math._unaryop(self, factor, "MUL", tsys)) |
---|
[1118] | 1348 | s._add_history("scale", varlist) |
---|
[876] | 1349 | print_log() |
---|
| 1350 | if insitu: |
---|
| 1351 | self._assign(s) |
---|
| 1352 | else: |
---|
[513] | 1353 | return s |
---|
| 1354 | |
---|
[876] | 1355 | def auto_quotient(self, mode='time', preserve=True): |
---|
[670] | 1356 | """ |
---|
| 1357 | This function allows to build quotients automatically. |
---|
| 1358 | It assumes the observation to have the same numer of |
---|
| 1359 | "ons" and "offs" |
---|
| 1360 | It will support "closest off in time" in the future |
---|
| 1361 | Parameters: |
---|
| 1362 | mode: the on/off detection mode; 'suffix' (default) |
---|
| 1363 | 'suffix' identifies 'off' scans by the |
---|
| 1364 | trailing '_R' (Mopra/Parkes) or |
---|
| 1365 | '_e'/'_w' (Tid) |
---|
[710] | 1366 | preserve: you can preserve (default) the continuum or |
---|
| 1367 | remove it. The equations used are |
---|
[670] | 1368 | preserve: Output = Toff * (on/off) - Toff |
---|
[1070] | 1369 | remove: Output = Toff * (on/off) - Ton |
---|
[670] | 1370 | """ |
---|
[876] | 1371 | modes = ["time"] |
---|
[670] | 1372 | if not mode in modes: |
---|
[876] | 1373 | msg = "please provide valid mode. Valid modes are %s" % (modes) |
---|
| 1374 | raise ValueError(msg) |
---|
| 1375 | varlist = vars() |
---|
[1070] | 1376 | s = scantable(self._math._auto_quotient(self, mode, preserve)) |
---|
[1118] | 1377 | s._add_history("auto_quotient", varlist) |
---|
[876] | 1378 | print_log() |
---|
| 1379 | return s |
---|
[710] | 1380 | |
---|
[1145] | 1381 | def mx_quotient(self, mask = None, weight='median', preserve=True): |
---|
[1141] | 1382 | """ |
---|
[1143] | 1383 | Form a quotient using "off" beams when observing in "MX" mode. |
---|
| 1384 | Parameters: |
---|
[1145] | 1385 | mask: an optional mask to be used when weight == 'stddev' |
---|
[1143] | 1386 | weight: How to average the off beams. Default is 'median'. |
---|
[1145] | 1387 | preserve: you can preserve (default) the continuum or |
---|
| 1388 | remove it. The equations used are |
---|
| 1389 | preserve: Output = Toff * (on/off) - Toff |
---|
| 1390 | remove: Output = Toff * (on/off) - Ton |
---|
[1141] | 1391 | """ |
---|
[1143] | 1392 | if mask is None: mask = () |
---|
[1141] | 1393 | varlist = vars() |
---|
| 1394 | on = scantable(self._math._mx_extract(self, 'on')) |
---|
[1143] | 1395 | preoff = scantable(self._math._mx_extract(self, 'off')) |
---|
| 1396 | off = preoff.average_time(mask=mask, weight=weight, scanav=False) |
---|
[1141] | 1397 | from asapmath import quotient |
---|
[1145] | 1398 | q = quotient(on, off, preserve) |
---|
[1143] | 1399 | q._add_history("mx_quotient", varlist) |
---|
[1145] | 1400 | print_log() |
---|
[1143] | 1401 | return q |
---|
[513] | 1402 | |
---|
[718] | 1403 | def freq_switch(self, insitu=None): |
---|
| 1404 | """ |
---|
| 1405 | Apply frequency switching to the data. |
---|
| 1406 | Parameters: |
---|
| 1407 | insitu: if False a new scantable is returned. |
---|
| 1408 | Otherwise, the swictching is done in-situ |
---|
| 1409 | The default is taken from .asaprc (False) |
---|
| 1410 | Example: |
---|
| 1411 | none |
---|
| 1412 | """ |
---|
| 1413 | if insitu is None: insitu = rcParams['insitu'] |
---|
[876] | 1414 | self._math._setinsitu(insitu) |
---|
[718] | 1415 | varlist = vars() |
---|
[876] | 1416 | s = scantable(self._math._freqswitch(self)) |
---|
[1118] | 1417 | s._add_history("freq_switch", varlist) |
---|
[876] | 1418 | print_log() |
---|
| 1419 | if insitu: self._assign(s) |
---|
| 1420 | else: return s |
---|
[718] | 1421 | |
---|
[780] | 1422 | def recalc_azel(self): |
---|
| 1423 | """ |
---|
| 1424 | Recalculate the azimuth and elevation for each position. |
---|
| 1425 | Parameters: |
---|
| 1426 | none |
---|
| 1427 | Example: |
---|
| 1428 | """ |
---|
| 1429 | varlist = vars() |
---|
[876] | 1430 | self._recalcazel() |
---|
[780] | 1431 | self._add_history("recalc_azel", varlist) |
---|
| 1432 | print_log() |
---|
| 1433 | return |
---|
| 1434 | |
---|
[513] | 1435 | def __add__(self, other): |
---|
| 1436 | varlist = vars() |
---|
| 1437 | s = None |
---|
| 1438 | if isinstance(other, scantable): |
---|
[876] | 1439 | print "scantable + scantable NYI" |
---|
| 1440 | return |
---|
[513] | 1441 | elif isinstance(other, float): |
---|
[876] | 1442 | s = scantable(self._math._unaryop(self, other, "ADD", False)) |
---|
[513] | 1443 | else: |
---|
[718] | 1444 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1445 | s._add_history("operator +", varlist) |
---|
[718] | 1446 | print_log() |
---|
[513] | 1447 | return s |
---|
| 1448 | |
---|
| 1449 | def __sub__(self, other): |
---|
| 1450 | """ |
---|
| 1451 | implicit on all axes and on Tsys |
---|
| 1452 | """ |
---|
| 1453 | varlist = vars() |
---|
| 1454 | s = None |
---|
| 1455 | if isinstance(other, scantable): |
---|
[876] | 1456 | print "scantable - scantable NYI" |
---|
| 1457 | return |
---|
[513] | 1458 | elif isinstance(other, float): |
---|
[876] | 1459 | s = scantable(self._math._unaryop(self, other, "SUB", False)) |
---|
[513] | 1460 | else: |
---|
[718] | 1461 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1462 | s._add_history("operator -", varlist) |
---|
[718] | 1463 | print_log() |
---|
[513] | 1464 | return s |
---|
[710] | 1465 | |
---|
[513] | 1466 | def __mul__(self, other): |
---|
| 1467 | """ |
---|
| 1468 | implicit on all axes and on Tsys |
---|
| 1469 | """ |
---|
| 1470 | varlist = vars() |
---|
| 1471 | s = None |
---|
| 1472 | if isinstance(other, scantable): |
---|
[876] | 1473 | print "scantable * scantable NYI" |
---|
| 1474 | return |
---|
[513] | 1475 | elif isinstance(other, float): |
---|
[876] | 1476 | s = scantable(self._math._unaryop(self, other, "MUL", False)) |
---|
[513] | 1477 | else: |
---|
[718] | 1478 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1479 | s._add_history("operator *", varlist) |
---|
[718] | 1480 | print_log() |
---|
[513] | 1481 | return s |
---|
| 1482 | |
---|
[710] | 1483 | |
---|
[513] | 1484 | def __div__(self, other): |
---|
| 1485 | """ |
---|
| 1486 | implicit on all axes and on Tsys |
---|
| 1487 | """ |
---|
| 1488 | varlist = vars() |
---|
| 1489 | s = None |
---|
| 1490 | if isinstance(other, scantable): |
---|
[876] | 1491 | print "scantable / scantable NYI" |
---|
| 1492 | return |
---|
[513] | 1493 | elif isinstance(other, float): |
---|
| 1494 | if other == 0.0: |
---|
[718] | 1495 | raise ZeroDivisionError("Dividing by zero is not recommended") |
---|
[876] | 1496 | s = scantable(self._math._unaryop(self, other, "DIV", False)) |
---|
[513] | 1497 | else: |
---|
[718] | 1498 | raise TypeError("Other input is not a scantable or float value") |
---|
[513] | 1499 | s._add_history("operator /", varlist) |
---|
[718] | 1500 | print_log() |
---|
[513] | 1501 | return s |
---|
| 1502 | |
---|
[530] | 1503 | def get_fit(self, row=0): |
---|
| 1504 | """ |
---|
| 1505 | Print or return the stored fits for a row in the scantable |
---|
| 1506 | Parameters: |
---|
| 1507 | row: the row which the fit has been applied to. |
---|
| 1508 | """ |
---|
| 1509 | if row > self.nrow(): |
---|
| 1510 | return |
---|
[976] | 1511 | from asap.asapfit import asapfit |
---|
[530] | 1512 | fit = asapfit(self._getfit(row)) |
---|
[718] | 1513 | if rcParams['verbose']: |
---|
[530] | 1514 | print fit |
---|
| 1515 | return |
---|
| 1516 | else: |
---|
| 1517 | return fit.as_dict() |
---|
| 1518 | |
---|
[484] | 1519 | def _add_history(self, funcname, parameters): |
---|
| 1520 | # create date |
---|
| 1521 | sep = "##" |
---|
| 1522 | from datetime import datetime |
---|
| 1523 | dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') |
---|
| 1524 | hist = dstr+sep |
---|
| 1525 | hist += funcname+sep#cdate+sep |
---|
| 1526 | if parameters.has_key('self'): del parameters['self'] |
---|
[1118] | 1527 | for k, v in parameters.iteritems(): |
---|
[484] | 1528 | if type(v) is dict: |
---|
[1118] | 1529 | for k2, v2 in v.iteritems(): |
---|
[484] | 1530 | hist += k2 |
---|
| 1531 | hist += "=" |
---|
[1118] | 1532 | if isinstance(v2, scantable): |
---|
[484] | 1533 | hist += 'scantable' |
---|
| 1534 | elif k2 == 'mask': |
---|
[1118] | 1535 | if isinstance(v2, list) or isinstance(v2, tuple): |
---|
[513] | 1536 | hist += str(self._zip_mask(v2)) |
---|
| 1537 | else: |
---|
| 1538 | hist += str(v2) |
---|
[484] | 1539 | else: |
---|
[513] | 1540 | hist += str(v2) |
---|
[484] | 1541 | else: |
---|
| 1542 | hist += k |
---|
| 1543 | hist += "=" |
---|
[1118] | 1544 | if isinstance(v, scantable): |
---|
[484] | 1545 | hist += 'scantable' |
---|
| 1546 | elif k == 'mask': |
---|
[1118] | 1547 | if isinstance(v, list) or isinstance(v, tuple): |
---|
[513] | 1548 | hist += str(self._zip_mask(v)) |
---|
| 1549 | else: |
---|
| 1550 | hist += str(v) |
---|
[484] | 1551 | else: |
---|
| 1552 | hist += str(v) |
---|
| 1553 | hist += sep |
---|
| 1554 | hist = hist[:-2] # remove trailing '##' |
---|
| 1555 | self._addhistory(hist) |
---|
| 1556 | |
---|
[710] | 1557 | |
---|
[484] | 1558 | def _zip_mask(self, mask): |
---|
| 1559 | mask = list(mask) |
---|
| 1560 | i = 0 |
---|
| 1561 | segments = [] |
---|
| 1562 | while mask[i:].count(1): |
---|
| 1563 | i += mask[i:].index(1) |
---|
| 1564 | if mask[i:].count(0): |
---|
| 1565 | j = i + mask[i:].index(0) |
---|
| 1566 | else: |
---|
[710] | 1567 | j = len(mask) |
---|
[1118] | 1568 | segments.append([i, j]) |
---|
[710] | 1569 | i = j |
---|
[484] | 1570 | return segments |
---|
[714] | 1571 | |
---|
[626] | 1572 | def _get_ordinate_label(self): |
---|
| 1573 | fu = "("+self.get_fluxunit()+")" |
---|
| 1574 | import re |
---|
| 1575 | lbl = "Intensity" |
---|
[1118] | 1576 | if re.match(".K.", fu): |
---|
[626] | 1577 | lbl = "Brightness Temperature "+ fu |
---|
[1118] | 1578 | elif re.match(".Jy.", fu): |
---|
[626] | 1579 | lbl = "Flux density "+ fu |
---|
| 1580 | return lbl |
---|
[710] | 1581 | |
---|
[876] | 1582 | def _check_ifs(self): |
---|
| 1583 | nchans = [self.nchan(i) for i in range(self.nif(-1))] |
---|
[889] | 1584 | nchans = filter(lambda t: t > 0, nchans) |
---|
[876] | 1585 | return (sum(nchans)/len(nchans) == nchans[0]) |
---|
[976] | 1586 | |
---|
| 1587 | def _fill(self, names, unit, average): |
---|
| 1588 | import os |
---|
| 1589 | from asap._asap import stfiller |
---|
| 1590 | first = True |
---|
| 1591 | fullnames = [] |
---|
| 1592 | for name in names: |
---|
| 1593 | name = os.path.expandvars(name) |
---|
| 1594 | name = os.path.expanduser(name) |
---|
| 1595 | if not os.path.exists(name): |
---|
| 1596 | msg = "File '%s' does not exists" % (name) |
---|
| 1597 | if rcParams['verbose']: |
---|
| 1598 | asaplog.push(msg) |
---|
| 1599 | print asaplog.pop().strip() |
---|
| 1600 | return |
---|
| 1601 | raise IOError(msg) |
---|
| 1602 | fullnames.append(name) |
---|
| 1603 | if average: |
---|
| 1604 | asaplog.push('Auto averaging integrations') |
---|
[1079] | 1605 | stype = int(rcParams['scantable.storage'].lower() == 'disk') |
---|
[976] | 1606 | for name in fullnames: |
---|
[1073] | 1607 | tbl = Scantable(stype) |
---|
| 1608 | r = stfiller(tbl) |
---|
[976] | 1609 | msg = "Importing %s..." % (name) |
---|
[1118] | 1610 | asaplog.push(msg, False) |
---|
[976] | 1611 | print_log() |
---|
[1118] | 1612 | r._open(name, -1, -1) |
---|
[976] | 1613 | r._read() |
---|
[1073] | 1614 | #tbl = r._getdata() |
---|
[976] | 1615 | if average: |
---|
[1118] | 1616 | tbl = self._math._average((tbl, ), (), 'NONE', 'SCAN') |
---|
[976] | 1617 | #tbl = tbl2 |
---|
| 1618 | if not first: |
---|
| 1619 | tbl = self._math._merge([self, tbl]) |
---|
| 1620 | #tbl = tbl2 |
---|
| 1621 | Scantable.__init__(self, tbl) |
---|
| 1622 | r._close() |
---|
[1118] | 1623 | del r, tbl |
---|
[976] | 1624 | first = False |
---|
| 1625 | if unit is not None: |
---|
| 1626 | self.set_fluxunit(unit) |
---|
| 1627 | self.set_freqframe(rcParams['scantable.freqframe']) |
---|
| 1628 | #self._add_history("scantable", varlist) |
---|
| 1629 | |
---|